Electing to bat first, Assam were in trouble straight away losing wickets at regular intervals to be 76 for six at lunch off 35 overs.
A patient 77 off 155 balls in 215 minutes with four fours by Gokul Sharma and useful contributions from Sukhvinder Singh (42 off 95 balls with four fours and a six) and Arlen Konwar (34 off 69 balls with three boundaries) helped them reach 167 for eight at tea.
However, Siddiqui, who claimed 250 Ranji wickets in his 62nd match, removed Rajkapoor Yadav for eight runs to end Assam's innings with another seamer Ranjit Khirid finishing with two for 23.
This is the 17th occasion that Siddiqui has taken five wickets in an innings.
At stumps, Maharashtra were 22 for no loss with openers Dheeraj Jadhav (13) and Marathe (7) at the wicket.
Brief scores: Assam first innings 201 all out (G Sharma 77, S Singh 42, A Konwar 34, I Siddiqui five for 68, K Adhav three for 41, R Khirid two for 23).